Uppsala Software Factory - X-UTIL Package

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Manuals

• AVEPDB to average models
• CELLO to play with your cell
• CT2HET to find hetero compounds in the PDB using only atom type and connectivity information (using the hetero-compound collection OMAC/hetero.pdb)
• DCUP to do quick calculations during data-collection
• HETZE to check the geometrical quality of hetero compounds (before or after refinement)
• MOLEMAN to do all sorts of things with/to PDB files (obsolete except for a few arcane options; use MOLEMAN2 instead !)
• MOLEMAN2 to do everything you used to do with MOLEMAN, but: better, stronger, faster !
• O2D to make 1D and 2D plots
• ODBM to analyse O datablocks (ODBMAN offers many more options !)
• ODBMAN to analyse O datablocks
• OOPS2 (OOPS is obsolete) to scrutinise your model and generate rebuilding macros for O
• PACMAN to check packing after Molecular Replacement
• RMSPDB to analyse multiple models (LSQMAN does this much better !)
• SEAMAN to generate search models for Molecular Replacement
• SOD to generate O datablocks from (aligned) sequences
• XPAND to expand molecules under NCS and/or spacegroup symmetry
• XPLO2D does "stuff" to X-PLOR input or output files; most popular for its option to auto-generate topology and parameter files for hetero-entities in X-PLOR
• XVRML to generate VRML files from PDB files
• Not documented yet: OST (superceded by SOD), ODLedit, PDB2CT

Examples

• MOLEMAN2
  • Example of a BFactor PLot (average).
  • Example of a BFactor PLot (radial).
  • Example of a OCcupancy PLot (average).
  • Example of a OCcupancy PLot (radial).
  • Example of a NUcleic DUarte_pyle plot (ACGTU).
  • Example of a PDb MC (Ramachandran) plot (labeled).
  • Example of a PDb CA ("CA-Ramachandran")plot (labeled).
  • Example of the use of an ONo DIsulfide ODL file in O.
  • Example of the use of an ONo CEll (solid) ODL file in O.
  • Example of the use of an ONo CEll (line) ODL file in O.
  • Example of the use of an ONo RIngs ODL file (protein) in O.
  • Example of the use of an ONo RIngs ODL file (nucleic acid) in O.
  • Example of the use of an ONo LS_plane ODL file in O.
  • Example of a DIstance PLot.
  • Example of a VRML display (of 1PMP) generated with MOLEMAN2.
• ODBMAN
  • Example of a PLot.
  • Example of the use of a 3D_odl ODL file in O.
  • Example of a SCatter plot.
• SOD
  • Example of a "CONS" CA-trace. Using task MULT and an alignment of 163 fasciculin sequences, SOD produces O datablocks and a macro. CONS is a CA-trace colour-ramped by the percentage conservation of the residue type that occurs in the structure compared to the complete set of sequences. Blue means little conservation, red means a lot.
  • Example of a "GRAD" CA-trace. See above for details. GRAD is a CA-trace coloured by the percentage conservation in steps of 20%.
  • Example of a "VARI" CA-trace. See above for details. VARI is a CA-trace colour-ramped by the number of different residue types at each position.
  • Example of a "ENTR" CA-trace. See above for details. ENTR is a CA-trace colour-ramped by the entropy at each alignment position.

Related freebies

• Trouble ftp-ing through your browser ? Look here !
• MOLEMAN2 server to generate Ramachandran, C-Alpha-Ramachandran, and Duarte-Pyle plots, as well as VRML worlds
• pre_oops.omac, an O macro that will do RS-fit, pep-flip and RSC and create datablock files needed for running OOPS(2)
• qalpha.omac, O macro for quick generation of arbitrarily long alpha-helices (uses MOLEMAN)
• qbeta.omac, O macro for quick generation of arbitrarily long beta-strands (uses MOLEMAN)
• plot_flip_rsc.csh, script that uses ODBMAN and O2D to produce plots of a pep-flip and an RSC-fit datablock file (including a scatter plot relating these two properties)
• het_dicts, script to generate dictionary files for a hetero compound from the hetero.pdb collection file
• multi_het_dicts, same as het_dicts, but extracts all examples of a hetero compound from structures solved at 2.0 Å resolution or better
• hetero.pdb, collection of many, many HETERO compounds extracted from the latest PDB release and all translated to (0,0,0)
• amore_solution.momac, MOLEMAN2 macro; almost fool-proof way to apply an AMORE solution
• bfac_stats.momac, MOLEMAN2 macro; list all sorts of statistics about your B-factors and make some plots
• make_vrml.momac, MOLEMAN2 macro; generates a cute VRML world (file) from any PDB file
• new_model.momac, MOLEMAN2 macro; go from an X-PLOR model to an O model and run quality checks and list B-factor statistics and create some useful O macros (e.g., to run pep-flip etc.) within a minute !
• o_to_xplor.momac, MOLEMAN2 macro; convert O model into PDB files suitable for X-PLOR *and* auto-generate an X-PLOR GENERATE input file
• plane.momac, MOLEMAN2 macro; generates an ODL file with a least-squares plane for a glucose residue (GLC; can be changed by editing the file, of course)
• prot_qual.momac, MOLEMAN2 macro; check some quality aspects of your protein
• xplor_to_ccp4.momac, MOLEMAN2 macro; convert X-PLOR model into PDB file suitable for O/CCP4
• rsr_cns_oops.csh, script to extract real-space R-values from CNS into an O-style datablock for use with OOPS(2)
• rfree.csh, script to produce PostScript plot of Rfree and Rcryst versus progress of X-PLOR refinement (uses O2D)
• o2dps, script for quick conversion of O2D plot files into PostScript or CricketGraph files
• Tutorial: Visualisation of planes. This explains how to visualise least-squares planes in O. The tutorial uses only Uppsala programs (MOLEMAN2 and O). In the example, a chain of nine twisting glucoses inside CBH I is visualised.

Description

Requirements

References

• GJ Kleywegt, JY Zou, M Kjeldgaard & TA Jones. International Tables for Crystallography, Volume F. Chapter 17.1, pp. 353-356, 366-367 (2001).
• GJ Kleywegt, J. Mol. Biol., 273, 371-376 (1997).
• GJ Kleywegt & TA Jones, Meth. Enzymol., 277, 208-230 (1997).
• GJ Kleywegt & TA Jones, Structure, 4, 1395-1400 (1996).
• GJ Kleywegt & TA Jones, Acta Cryst., D52, 829-832 (1996).
• GJ Kleywegt & TA Jones, Structure, 4, 1395-1400 (1996).